ts: Write a white paper / implementation document for tree seq encoding and interaction with AlphaSimR #16
Description
We already have a number of issues related to this, but we never set out to do a document to clarify what we want/need, hence this issue:
- ts: Save original recombination position for tree sequence recording ts: Save original recombination position for tree sequence recording #6
- ts: Add/use seqLength to properly work with tree sequences ts: Add/use seqLength to properly work with tree sequences #9
- ts: Saving AlphaSimR specific metadata and provenance information ts: Saving AlphaSimR specific metadata and provenance information #13
- ts: How will we handle tskit nucleotide/integer position vs. float position vs. AlphaSimR marker position? ts: How will we handle tskit nucleotide/integer position vs. float position vs. AlphaSimR marker position? #10
- ts: Storing time/generation forward in time ts: Storing time/generation forward in time #11
- ts: TreeSequence class (individual table) can hold parents - capture this information as well ts: TreeSequence class (individual table) can hold parents - capture this information as well #8
- ts: How will we encode node and individual IDs? ts: How will we encode node and individual IDs? #12
Studying tskit code I see that when exporting to Nexus, Newick, or FASTA files, it uses n0, n1, ... type naming for node IDs. Not sure if relevant for us.
Useful docs on requirements to get a valid tree sequence: https://tskit.dev/tskit/docs/stable/data-model.html#sec-valid-tree-sequence-requirements
@LynxJinyangii has already done quite a bit of exploration and prototyping at https://github.com/LynxJinyangii/AlphaSimR/blob/master/dev/notesRealBreakpoints.md
We effectively want something like what Ben Haller did with his document https://github.com/MesserLab/SLiM/blob/master/treerec/implementation.md, but that document merges the initial white paper (=plan) and later implementation, so we will end up with such a doc at the end, but we need a clear plan first and then implementation.